From 55537c0d1e95b02dd56fe45895031a63d9cc34c9 Mon Sep 17 00:00:00 2001 From: asivache Date: Thu, 16 Apr 2009 16:51:00 +0000 Subject: [PATCH] chnage class name, now it compiles... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@451 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/playground/indels/IndelInspectorMain.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java b/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java index 8070c3e26..b066b1c35 100755 --- a/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java +++ b/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java @@ -17,7 +17,7 @@ import edu.mit.broad.picard.reference.ReferenceSequence; import net.sf.samtools.*; import org.broadinstitute.sting.utils.GenomeLoc; -public class IndelInspector extends CommandLineProgram { +public class IndelInspectorMain extends CommandLineProgram { // Usage and parameters @Usage(programVersion="1.0") public String USAGE = "Investigates indels called in the alignment data\n"; @@ -34,7 +34,7 @@ public class IndelInspector extends CommandLineProgram { /** Required main method implementation. */ public static void main(final String[] argv) { - System.exit(new IndelInspector().instanceMain(argv)); + System.exit(new IndelInspectorMain().instanceMain(argv)); } protected int doWork() { @@ -110,7 +110,6 @@ public class IndelInspector extends CommandLineProgram { if ( location == null || GenomeLoc.compareContigs(cur_contig, location.getContig()) == 0 ) { contig_seq = reference.get(r.getReferenceIndex()); String refstr = new String(contig_seq.getBases()); - col.setReferenceSequence(refstr); if (!CONTROL_RUN) pileBuilder.setReferenceSequence(refstr); System.out.println("loaded contig "+cur_contig+" (index="+r.getReferenceIndex()+"); length="+contig_seq.getBases().length+" tst="+contig_seq.toString()); }